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Chem Bio > CHEM BIO 2 > Flashcards

CHEM BIO 2 Flashcards

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1
Q

How does bacterial transcription differ from eukaryotic

A

bacteria is done next to ribosome translated
immediately,
bacterial 5’end is a triphosphate
eukaryotic - done in nucleus and transported out ,
2) it has introns to be removed or kept in,
3) has 5’ capping and
4) has poly a tail post transcriptionally

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2
Q

Why do we splice mRNA

A

biodiverstiy

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3
Q

What and why do we have a 5’ g cap

A

It is literally GTP applied to the 5 end - Protects the end, disguises it as a 3’ end , prevents degradation and is a (ESSENTIAL FOR LOADING) binding site for ribosome

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4
Q

Why do we have poly A tail

A

direct mRNA to ribosome - - comes from a POLY A polymerase binder - 50-200 A’s

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5
Q

Know RNA processing steps

A

draw it out - pol II binds , as soon as transcribed - cap installation - then splicing occurs at splice site - once released - poly A tail from polyemrase - then exported to ribosome - cap and poly a tail have protein protein interactions - then DECAP - marks it for degradation

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6
Q

What does ribonuclease H do

A
  • removes RNA primers from DNA replications - recognizes RNA-DNA hybrid and cuts out RNA - high specificity - good in lab(eg if mRNA pathogenic - can bind antisense DNA and cut it out
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7
Q

Can phosphates be chiral

A

yeah

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8
Q

What reaction does the ribosom ecatalyze

A

aminolysis of alpha amino esters (SIMPLE KNOW HOW TO DRAW)

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9
Q

What catalyzes the aminolysis of alpha amin esters

A

Lone pair on N3 of adenine deprotonates amino group (pKa ~7.6, over 10,000x more basic than N3 of free A due to H-bonding
)

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10
Q

What is energy used for in protein synth

A

In moving them along the protein and fideltiy

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11
Q

Are amino acids checked?Relevance?

A

NOPE only based on codon anti codon - SO if can generate an amino acid with the right codon ou can stick whatever you want on there to be added

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12
Q

What is tRNA synthase responsible for

A

f9idletiy of translation - couplesATP to amino acylation and 2 active site can have different specificity - this ATP attachment is largely done by attaching AMP to something - it’s a good leaving group

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13
Q

Using ATP for an nufvaroable reaction - particular joining amino acid to trna

A

so ATP binds to amino acid but the pyrophosphate cleaves off - has AMP as a good leaving group so tRNA can attach 9know how to draw - tRNA synthase slide - in notes)

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14
Q

What is a riboswitch

A

regions on the nascent 3’ RNA THAT CAN BIND SMALL MOLECULES THAT AFFECT translationg - 2 important regions are the termination sequence and aptarmer site which is a ligand binding site - - can cause conformation changes to terminate transcription
t

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15
Q

are peptide sequences directional?

A

yeah

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16
Q

PRACTICE TELLING IS AN AMINO ACID IS CHARGED OR NOT GIVEN ITS PKA

A
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17
Q

Most important force for protein folding and name 3 examples

A

Non polar interactions such as arene-arene, cation pi, dispersive, much more common than H bonds and salt bridges

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18
Q

What are most often the conserved parts of protein structure

A

hydrophobic core

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19
Q

What are the general forces that control protein secondary and tertiary structure

A

H-bonds
Dipoles
Sterics
Hydrophobic effect

BUT sterics and dipoles real important

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20
Q

Go over the sterics/ and A12 vs A3 strain again

A

Know how to draw it - so the A13 comes from the phi bond on the next main oacid and A12 comes from the not phi strain of the same amino acid (can tell byh counting bonds A13 should have 4 bonds total, A12 3) and A13 is the one that is really defining the energy and shape of peptide

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21
Q

Go over the sterics/ and A12 vs A3 strain again

A

in notes

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22
Q

What is the arrangement for alpha helix in terms of h bonding and why (what are other possible(

A

i + 4 - most stable (h bond angle matters) i+3 makes a 3:10 helix and i + 2 makes a serpentine shape - gamma turn s- not often used

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23
Q

Alpha helix macrodipoles - describe them

A

From the N to C terminal have + to negative general macrodipole

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24
Q

amino acids with issues with alpha helix

A

Proline, glycine and beta branched hydrophobics

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25
Q

What are the turns you can make and what do they depend on (peptide chains)

A

Beta (180 degree turn) and gamma turn (90 degree) - beta is an I and i+3 H bond whereas gamma is an I and I+2 h bond

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26
Q

where are majro structures on ramachandran plot

A

see notes

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27
Q

cysteine vs cystine (which direction redox)

A

unbonded vs disufide bridge -reducing seperates them oxidative conditions bind them

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28
Q

Some basic protein motifs

A

Leucine zipper and zinc finger bind DNA, beta sandwiches are common architecture, collagen triple left handed helix, 7 TM and beta barrel span membranes

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29
Q

Beta branched amino acids means what for structure?

A

Bad for alpha helices good for beta sheets

30
Q

What aere our two activation energies in our energy plot for an enzyme

A

There’s Ea from initial to largest peak - and this is km/cat - this is assuming [S] is limited BUT if [s] is saturated we have Ea kcat - which is just based on enzyme turnover (from 1sts stable state to second peak
either can be the slow step

31
Q

Wht is km mathematically

A

kcat + k-1 / k1 (can think of as things moving away from ES divided by constant moving towards Es

32
Q

Why do we use Kcat/km

A

for enzyme efficiency - use this because Km can vary so much by various terms hard to just pin point what is making km small

33
Q

What is kcat/km

A

Slope of our [s] vs ks plot - 2nd order constant

34
Q

If we add an inhibitor that effects E (instead of E +S we get E+I lowers its initial energy) what are the changes and how does that change our various plots (energy diagram, [s] plot)

A

so it will increase our activation energy (the initial condition is at a lower energy - BUT note it only changes our first Ea (ea kcat/km?) I guess as opposed to just Ea Kcat because the the stable intermediate to the transition state of forming the product is in the same place so that ea doesn’t change. ON our [s] plot - it changes the initial slop because that’s kcat/km and km is increasing now -

35
Q

What are the phi and trident angles

A

phi is between N and R and trident is between O and R- Phi is A12 hinderance and trident is A13 hinderance (bigger - A13 is 2 apart and a12 is 1 apart)

36
Q

Phi and trident angles for common motifs

A

-90, 150 for Beta pleated and -90, -60 for alpha helices

37
Q

What is kd mathematically

A

Koff / Kon

38
Q

Are alpha helices stabilized by h bonds between backbone amides int he same hellix? true or false

A

True

39
Q

Are glycines commonly found in alpha helices?

A

No, because glycine so flexible can break helices

40
Q

Are the amino acid side chains in a beta sheet all facing the same direction

A

No

41
Q

Are beta sheets held together by h bonds between back bone amides in different strands?

A

Yes

42
Q

Native peptide ligation requires what on the N terminus

A

a Cystine

43
Q

What are the beta branched amino acids

A

Valine isoleucine threonine

44
Q

what makes a leucine zippe

A

a leuceine every 7 amino acids

45
Q

2 key assumptions for michaelis menten

A

1) product formation concentration is so low it’s negligible and the product binding to enzyme is negligible/non existent and 2) formation and breakdown of ES is equivalent such that ES is constant

46
Q

What are the axes on a lineweaver burke plot

A

1/[s] and 1/vo

47
Q

On a line weaver burke plot where are the key points

A

The x intercept is -1/km with competitiv inhibition km increases so this point gets closer to 0, The y intercept is -1/Vm - so when we get uncompetitive inhibition this changes

48
Q

Uncompetitive inhibitor snad non (mixed) competitive inhibitors effect on Km and vmax

A

uncompetitive inhibitors decrease Vmax AND km, while mixed decrease Vmax and sometimes Km

49
Q

Whats the equation for competitive inhibition

A

V = Vmax [S] / (Km(1+[I]/Ki) + [S])

50
Q

What do the followig co factors do:
Folate
S-adenylmethionine
Nicotinamide Adenine Dinucleotide
Pyridoxal Phosphate
Biotin
Thymine Pyrophosphate

A

Folta carries one carbon units (methyl, formyl, methylene to transfer to other molecules)
S-adenylmethionine - transfers one carbon as methyl and provides for enzymes as a donor)
NAD NADH - redox reactions
Pyridoxal Phosphate - catalyzes reactions for racemization, decarboxylation and deamination of amino acids
Biotin - transports carboxylate groups between active sites
Thymine Pyrophosphate - thiazolium carbon nucleophile can attack carbonyls, stabilizes carbanions for biosynth orcatabolic reactions

51
Q

Delta G from energy plot

A

Efwd - e rev (which is startig state to apex)

52
Q

Other consdierations in rate experiments

A

How much of enzyme actually active (does []= [] of active enzyme) and also want substrate way bigger than enzyme amount such that the amount of substrate lost is negligible (so don’t need to factor in “free remaining R” should be very similar to initial cncentration

53
Q

What is the equation for v

A

]vmax*[s] / (km + [s] (so this way when [s] = km v is 1/2 vmax

54
Q

kcat vs kcat/km for rate constants

A

kcat is 1st order rate oconstant at saturated [s], whereas kcat/km is the 2nd order rate constant for free enzyme and free s

55
Q

does tyrosine have a pka?

A

yeah

56
Q

what does coenzyme A do

A

acyl group carrier

57
Q

NAD+ /NADPH

A
58
Q

Are dissociations unimolecular

A

you bet

59
Q

T/F for pH sensitive in terms of binding

A

I guess can just say yes i fknown histidine

60
Q

Both parallel and anit parallel beta plested sheets are stabilized through h bonds of backbone amides from 2 or more beta sheets (T/fF)

A

true

61
Q

peptide vs invivo systnheises

A

peptide is C to N (as in new amino acids are their C to the existing N); in vivo its N to C in which amino acids add their N to the existing C

62
Q

Zn 2+ in catalytic site

A

Acts as lewis acid - can active carbonyl for attack

63
Q

test for Kd experiment for competitive binding

A

AN equillibiurm binding assay - compare concentraiton bound figure out Kd in presence of and wihtout inhibitor

64
Q

How does PLP work

A

aldehyde - forsm imine with amino acid - conjugated bond system - acitvates bond next to imine

65
Q

Mechanism based vs transition state inhibitor

A

mechanism based more ikely to interact with functional groups in active site - make covalent bonds - both bind in active site tho

66
Q

FOr a small molecule which is more important k off or k on

A

k off

67
Q

What is Vmax

A

The rate under saturated substrate

68
Q

uncompetitive vs non competitive

A

Non-competitive inhibitors bind equally well to the enzyme and enzyme–substrate complex. Uncompetitive inhibitors bind only to the enzyme–substrate complex - uncompetitive lower both kcat AND km (kcat/km stays the same) non competitive inhibitors decrease Kcat and don’t effect Km so kcat/km goes down

69
Q

All the inhibition types and effects on graphs

A

Competitive - increase Km - kcat the same (so for lineweaver burke - more inhibited means smaller x intercept - y intercept the same)
uncompetitive - Decreases Km AND kcat - So as we increase inhibition x intercept actually gets bigger AND our y intercept gets bigger
Non competitive - decreases Kcat keeps Km the same - so should all have same x intercept but y intercept gets bigger with more inhibition
Mixed competitive - Km can get bigger vmax can get bigger - so with more Inhibition x intercept gets smaller (km bigger) and vmax smaller (y intercept bigger)

70
Q

NAD+ vs NADP

A

NAD+ for catabillic, NADPH for analbolic

Chem Bio (17 decks)

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